Contacts of the strand formed by residues 394 - 397 (chain A) in PDB entry 5EQX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ILE* 3.6 45.4 - - + +
358A GLY* 3.7 9.2 - - - +
359A THR* 4.2 8.5 - - - +
387A MET 3.6 1.0 - - - +
388A ILE* 3.3 2.8 - - - -
389A ASP* 2.8 31.1 + - + +
392A THR* 3.1 22.3 + - - +
393A ALA* 1.3 78.9 - - - +
395A ILE* 1.3 59.6 + - - +
396A LYS* 4.1 8.5 + - + +
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A PHE* 4.3 9.0 - - + -
356A ILE* 3.4 1.8 - - - -
357A LEU* 2.5 51.1 + - + +
358A GLY 2.9 17.6 + - - +
360A TYR* 4.1 24.2 - - + -
378A MET* 4.3 4.5 - - + -
386A LEU* 4.0 23.3 - - + -
387A MET 3.3 6.7 - - - +
388A ILE* 4.1 10.8 - - + -
393A ALA 3.8 6.3 - - - +
394A GLU* 1.3 77.6 - - - +
396A LYS* 1.3 67.2 + - - +
417A VAL* 4.3 11.2 - - + -
432A VAL* 4.2 22.2 - - + -
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Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ASP* 3.6 35.8 + - - +
355A TYR 3.8 7.6 - - - +
356A ILE* 4.0 29.7 - - + +
386A LEU* 3.4 7.3 - - - +
387A MET* 2.9 35.4 + - + +
394A GLU* 5.1 7.6 - - + +
395A ILE* 1.3 81.7 - - - +
397A PHE* 1.3 68.2 + - - +
398A VAL* 4.9 4.7 - - + -
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A VAL* 5.3 4.0 - - + -
352A LEU* 3.1 51.6 - - + +
353A VAL* 4.0 5.2 - - - +
354A ASP* 3.5 16.2 + - - +
355A TYR* 3.5 29.9 + + + +
357A LEU* 3.9 26.0 - - + -
385A TYR* 3.3 27.1 - + + -
386A LEU* 4.0 16.4 - - + -
396A LYS* 1.3 78.2 - - - +
398A VAL* 1.3 69.7 + - - +
399A LYS 3.8 19.3 - - - +
413A ILE* 4.2 16.6 - - + -
434A VAL* 4.3 8.7 - - + -
436A VAL* 5.5 4.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il